Nine contact

## AA Ninemers contact position, changes FROM AA X
NINE_CONTACT_FROM_PLT=readRDS(file="NINE_CONTACT_FROM_PLT.rds")+theme_pubr(base_size=16)
NINE_CONTACT_FROM_PLT

## AA Ninemers contact position, changes TO AA X
NINE_CONTACT_TO_PLT=readRDS(file="NINE_CONTACT_TO_PLT.rds")+theme_pubr(base_size=16)
NINE_CONTACT_TO_PLT

## Specific mutation change, ninemers contact postion
NINE_CONTACT_TO_SPECIFICMUT_PLT=readRDS(file="NINE_CONTACT_TO_SPECIFICMUT_PLT.rds")+theme_pubr(base_size=16)+rotate_x_text()
NINE_CONTACT_TO_SPECIFICMUT_PLT

Ten contact

## AA TEN contact position, changes FROM AA X
TEN_CONTACT_FROM_PLT=readRDS(file="TEN_CONTACT_FROM_PLT.rds")+theme_pubr(base_size=16)
TEN_CONTACT_FROM_PLT

## AA TEN contact position, changes TO AA X
TEN_CONTACT_TO_PLT=readRDS(file="TEN_CONTACT_TO_PLT.rds")+theme_pubr(base_size=16)
TEN_CONTACT_TO_PLT

# Ten change to AA AND POS
TEN_CONTACT_TO_AA_POS_PLT=readRDS(,file="TEN_CONTACT_TO_AA_POS_PLT.rds")+theme_pubr(base_size=16)+rotate_x_text()
TEN_CONTACT_TO_AA_POS_PLT

Epitope escape potential

ESCAPE_POT_PER_PEPTIDE_PLT=readRDS(file="ESCAPE_POT_PER_PEPTIDE_PLT.rds")#+theme_pubr(base_size=16)+rotate_x_text()
ESCAPE_POT_PER_PEPTIDE_PLT

Hydrophobicity vs. transition potential

HYDROPHOBICITY_ANCHORFREQ_PLT=readRDS(file="HYDROPHOBICITY_ANCHORFREQ_PLT.rds")
HLA_TRANSITIONPOT_GRPS_PLT=readRDS(file="HLA_TRANSITIONPOT_GRPS_PLT.rds")
AA_COMP_TRANSITIONPOT_GRPS=readRDS(file="AA_COMP_TRANSITIONPOT_GRPS.rds")

HLA_TRANSITIONPOT_GRPS_PLT
## Warning in wilcox.test.default(c(6, 2, 30, 7, 19, 18, 10, 19, 17), c(3, : cannot
## compute exact p-value with ties

A_GRID = cowplot::plot_grid(NINE_CONTACT_FROM_PLT, NINE_CONTACT_TO_PLT, nrow=1)

B_GRID = cowplot::plot_grid(NINE_CONTACT_TO_SPECIFICMUT_PLT+theme(legend.position = "none"), nrow=1)


C_GRID = cowplot::plot_grid(TEN_CONTACT_FROM_PLT+theme(legend.position = "none"), TEN_CONTACT_TO_PLT+theme(legend.position = "none"), nrow=1)

D_GRID = cowplot::plot_grid(TEN_CONTACT_TO_AA_POS_PLT+theme(legend.position = "none"), nrow=1)

E_GRID = cowplot::plot_grid(ESCAPE_POT_PER_PEPTIDE_PLT, nrow=1)

F_GRID = cowplot::plot_grid(HYDROPHOBICITY_ANCHORFREQ_PLT, NULL, nrow=1, ncol=2, rel_widths = c(1, 2))
## Warning in wilcox.test.default(c(1, 1, 0.333333333333333, 0.666666666666667, :
## cannot compute exact p-value with ties
F_GRID_ii = cowplot::plot_grid(AA_COMP_TRANSITIONPOT_GRPS, NULL, nrow=1, ncol=2, rel_widths = c(1, 2))


F_GRID = cowplot::plot_grid(HYDROPHOBICITY_ANCHORFREQ_PLT, HLA_TRANSITIONPOT_GRPS_PLT,AA_COMP_TRANSITIONPOT_GRPS,nrow=1, ncol=3)
## Warning in wilcox.test.default(c(1, 1, 0.333333333333333, 0.666666666666667, :
## cannot compute exact p-value with ties
## Warning in wilcox.test.default(c(6, 2, 30, 7, 19, 18, 10, 19, 17), c(3, : cannot
## compute exact p-value with ties

```{,dpi=300, fig.width = 24,fig.height=28}

cowplot::plot_grid(A_GRID, B_GRID, C_GRID, D_GRID, E_GRID,F_GRID,F_GRID_ii, nrow = 7, align=“v”, axis=“bt”, rel_heights = c(0.9,0.9,0.9,0.9,1.2,1.2,1))



```r
cowplot::plot_grid(A_GRID, B_GRID, C_GRID, D_GRID, E_GRID,F_GRID, nrow = 6, align="v", axis="bt",
                   rel_heights = c(0.9,0.9,0.9,0.9,1.2,1.2))

supplementary

NINE_CONTACT_SCATTER_PLT=readRDS(file="NINE_CONTACT_SCATTER_PLT.rds")

TEN_CONTACT_SCATTER_PLT=readRDS(file="TEN_CONTACT_SCATTER_PLT.rds")

cowplot::plot_grid(NINE_CONTACT_SCATTER_PLT,TEN_CONTACT_SCATTER_PLT, NULL,NULL, nrow=1,
                   rel_widths = c(0.25,0.25,0.25,0.25))